Upgrading to MiniSeq Control Software v2
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**What is the upgrade?**The MiniSeq system upgrade is accomplished by updating to MiniSeq Control (MnCS) v2. MnCS v2 provides several enhancements:
Changes the Operating System to Windows 10
Updates MiniSeq System Suite to version 2
Includes installation of a new hard drive
Is performed by an Illumina Field Service Engineer
Software changes with the MiniSeq System Suite v2 are found in the . The most up-to-date Windows 10 upgrade information for all Illumina Sequencing Systems is found on the page.
Upgrade process
To upgrade the MiniSeq to Windows 10 and MiniSeq System Suite v2, contact with the instrument serial number.
The field support team will then contact you to coordinate and schedule the upgrade.
If the MiniSeq has an active service contract or first-year warranty, the upgrade is provided at no additional cost.
Upgrades are available for instruments not on a service contract as a billable service.
After the upgrade, the control software cannot be downgraded to the previous version.
Run setup with MiniSeq Control Software v2
Runs can be set up using Local Run Manager (LRM) or Manual mode. Both options can upload runs to BaseSpace Sequence Hub (BSSH) for Run Monitoring or Monitoring and Storage. Instructions for run setup are found in the .
Note: Currently, only LRM accounts with admin-level permissions can start runs using LRM if user management is enabled. Please see the Knowledge Base for more information.
The previous LRM (v1.0) modules used on the MiniSeq System Suite v1.x are not compatible with LRM 2.4.1. To download the new modules, visit the page and run the installers using an admin account.
Sample sheet i5 primer orientation
In Local Run Manager mode, always enter the i5 sequence in the forward orientation, no matter which instrument type you are using. Local Run Manager will generate a final sample sheet with the i5 sequence in the correct orientation depending on the instrument type.
In Manual mode, the attached sample sheet is copied to the output location (including BaseSpace Sequence Hub) without validation or conversion of the indexes. This means that the i5 sequence must be in the final orientation, which for the NextSeq and MiniSeq, is the reverse complement orientation.
Former BaseSpace PrepTab Users
BaseSpace PrepTab is no longer supported in MiniSeq Control Software v2. To upload a run directly to BaseSpace, use Manual Mode or LRM mode with Run Monitoring and Storage.
First run after upgrade
During the first run after the upgrade, the flow cell registration step of the pre-run check can take longer (about 20 minutes). After the first run, the pre-run check time will go back to normal.
Networking considerations
Duplicate run folders
Resources:
On the NextSeq 500/550, MiniSeq, and iSeq 100, the second index (i5) is read in the orientation compared to the MiSeq. The correct orientation to enter the i5 index depends on the instrument run mode:
When the first run is completed, a prompt may appear asking to upload Operational Qualification results to BSSH. Until a selection is made, the run will still show as “Analyzing” in BSSH. Select Don’t Ask Again to keep this prompt from reappearing.
Setting the output folder to a network location has special considerations due to Windows 10 authentication requirements. To configure the network properly, work with your IT team and follow the instructions in the Knowledge Base article
Occasionally, LRM may create a duplicate run folder with a second set of analysis files. Monitor hard drive space and delete these extra run folders if needed.
For any feedback or questions regarding this article (Illumina Knowledge Article #2699), contact Illumina Technical Support .
